Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020881.1 Corchorus olitorius cultivar O-4 contig20914, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9695
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Found at i:972 original size:319 final size:316
Alignment explanation
Indices: 487--1277 Score: 869
Period size: 319 Copynumber: 2.5 Consensus size: 316
477 AAAATTTTGC
* * * * **
487 AAAACTGACTTGAACAATTTTTCCTCAATTCTTAGCCACAATACTTTGAAAAAATATATAATTCA
1 AAAACTGAC-TGAA-AATTTTTTCTTAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCA
* * * * * *
552 ATGCCAATAA-ATTGAAGGGTTTTTGACACTTATAATATCGTTTTTCCATTTTTTTCCGAATTTA
64 AAGCCAAAAAGATTG-AGGGATTTTCACACTTCTAATATCGTTTTTCCATTTTTTT-CGAATTAA
* * *
616 TTTTTACTTAAATCGAAACAAGATTTAAATACTCGT-AAAACAAATCCTTAAATCTATTGTGGCT
127 TTTCTAATTAAATCGAAACAAGATTTAAATACTCGTAAAAACAAATCCTTAAATCTAATGTGGCT
* * *
680 GAGATTTGGTTAGATGA-ATAAAGATATATCAAGGAGTCTTT-CTATCAAAAATCATGCAAAATT
192 G-GATTTGATTAGAT-ATATAAAGATATATCAAGGAGTATTTGC-ACCAAAAATCATGCAAAATT
*** * * *
743 GAG-TGGGGCACCTA-AACGCGTTTTTTGCCCAAAACCGTGATGGTTAGTACACGATTTCGGCTA
254 GAGCCAAGGCACC-AGAACGCG-TTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGCTA
*
806 AAAACTGACTGAAAATTTTTTTCTTAATTTTTTGCAACAATACTCAGAAAAAAATATATAATTCA
1 AAAACTGACTGAAAA-TTTTTTCTTAATTTTTTGCCACAATACTCAG-AAAAAATATATAATTCA
* * *
871 ACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTTCCA-CTTTTTCAGAATTAA
64 AAGCCAAAAAGATTGA-GGGATTTTCACACTTCTAATATCGTTTTTCCATTTTTTTC-GAATTAA
* * * * *
935 TTTCTAATTTAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCTAATGTGGCT
127 TTTCTAATTAAATCGAAACAAGATTTAAATACTCGTAAAAACAAATCCTTAAATCTAATGTGGCT
* * * * * *
1000 GGATTTGATTTGATATTTATAGATATTTCAAGGAGTATTTGCGCCAAAAATCATGCAAAATTTAG
192 GGATTTGATTAGATATATAAAGATATATCAAGGAGTATTTGCACCAAAAATCATGCAAAATTGAG
* *
1065 CCAAGGCTCCAGAACGCGTTTTAGCCAAAAACCATTATGGTTAGTACACGATTTCGGCTA
257 CCAAGGCACCAGAACGCGTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGCTA
** * * * *
1125 AAAACTGACCCAAAAAGATTTTTCTCT-ATTTATTGCCACAATACTCATAAAAAATATATAATCC
1 AAAACTGA-CTGAAAA-TTTTTTCT-TAATTTTTTGCCACAATACTCAGAAAAAATATATAATTC
* * ** * *
1189 AAAGCCAAAAGGATGGAAAGATTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCGAATTAAT
63 AAAGCCAAAAAGATTGAGGGATTTTCACACTTCTAATATCGTTTTTCCATTTTTTTCGAATTAAT
* * * *
1254 TTCTACTCAGATCGAAAAAAGATT
128 TTCTAATTAAATCGAAACAAGATT
1278 CAGATATTTC
Statistics
Matches: 398, Mismatches: 61, Indels: 27
0.82 0.13 0.06
Matches are distributed among these distances:
317 2 0.01
318 84 0.21
319 209 0.53
320 102 0.26
321 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (316 bp):
AAAACTGACTGAAAATTTTTTCTTAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAA
GCCAAAAAGATTGAGGGATTTTCACACTTCTAATATCGTTTTTCCATTTTTTTCGAATTAATTTC
TAATTAAATCGAAACAAGATTTAAATACTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGGAT
TTGATTAGATATATAAAGATATATCAAGGAGTATTTGCACCAAAAATCATGCAAAATTGAGCCAA
GGCACCAGAACGCGTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGCTA
Found at i:1960 original size:324 final size:322
Alignment explanation
Indices: 1440--2096 Score: 781
Period size: 324 Copynumber: 2.0 Consensus size: 322
1430 CAATACTTTG
* * *
1440 AAAAAATATATAATTCAATGCCAAAAAATTGAAGGGTTTTTGATACTTATAATATTGTTTTTCCA
1 AAAAAATATATAATTCAACGCCAAAAAATTGAAGGGTTTTTGACACTTATAATATCGTTTTTCCA
* *
1505 TTTTTTTCGAATTTATTTCTAATTAAATCAAAACTAGATTCAGATACTCGTAAAAACAAATCCTT
66 TTTTTTTCGAATTAATTTCTAATTAAATCAAAACTAGATTCAGATACTCGAAAAAACAAATCCTT
* * * *
1570 AAATCCATTGTAGATAAGATTTGGTTAGATGAATAAAGATATTTCAAGGAATCTTTCTGCCAAAA
131 AAATCCAATGTAGACAAGATTTGCTTAGATGAATAAAGATATTTCAAGGAATATTTCTGCCAAAA
* * * **
1635 ATCATGCAAAATTGAGTGGGGGCTCC-GAAACGCGTTTTTTGC-CCAAAACCGTGATAGTTAGTA
196 ATCATGCAAAATTGAGTCGGGGCTCCAG-AACGC-ATTTTAGCAAAAAAACCGTGATAGTTAGTA
* * *
1698 CACGATTTCGGCTAAAAACTGA-ATGAAAAATTTTTTCTTAATTTTTCGCAACAATACTCAGAA
259 CACGATTTCGGCTAAAAACTGACACGAAAAATTTTTTCTCAATTTTTCACAACAATACTCAGAA
* * *
1761 AAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTTTACACTTCTAATATCGTTTTTC
1 AAAAAATATATAATTCAACGCCAAAAA-ATTGAAGGG-TTTTTGACACTTATAATATCGTTTTTC
* * * * *
1826 CATTTTTTTCAGAATTAATTTCTAATTTAATCGAAA-TAAGATTTAGATGCTCGAAAAAACATAT
64 CATTTTTTTC-GAATTAATTTCTAATTAAATCAAAACT-AGATTCAGATACTCGAAAAAACAAAT
* * * * * * *
1890 CCTTATATCTAATG-AGGCAGAGGTTTGACTT-GAT-ATTTATAGATATTTCAAGGACTATTTGC
127 CCTTAAATCCAATGTAGACA-AGATTTG-CTTAGATGA-ATAAAGATATTTCAAGGAATATTT-C
* *
1952 -GGCAAAAATCATGCAAAATTGAGTCGGGGCTCCAGAACGCATTTTAGCAAAAAAAACCGTGATG
188 TGCCAAAAATCATGCAAAATTGAGTCGGGGCTCCAGAACGCATTTTAGC-AAAAAAACCGTGATA
* * * * * *
2016 GTTAGTATACGATTTCGGCTAAAAACTTACCCGAAAAGTTTTTTCTCAATTTTTTACCACAATAC
252 GTTAGTACACGATTTCGGCTAAAAACTGACACGAAAAATTTTTTCTCAATTTTTCACAACAATAC
*
2081 TCATAA
317 TCAGAA
*
2087 AAAATATATA
1 AAAAAATATA
2097 ATCCAAACCC
Statistics
Matches: 282, Mismatches: 42, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
321 26 0.09
322 8 0.03
323 44 0.16
324 120 0.43
325 42 0.15
326 42 0.15
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (322 bp):
AAAAAATATATAATTCAACGCCAAAAAATTGAAGGGTTTTTGACACTTATAATATCGTTTTTCCA
TTTTTTTCGAATTAATTTCTAATTAAATCAAAACTAGATTCAGATACTCGAAAAAACAAATCCTT
AAATCCAATGTAGACAAGATTTGCTTAGATGAATAAAGATATTTCAAGGAATATTTCTGCCAAAA
ATCATGCAAAATTGAGTCGGGGCTCCAGAACGCATTTTAGCAAAAAAACCGTGATAGTTAGTACA
CGATTTCGGCTAAAAACTGACACGAAAAATTTTTTCTCAATTTTTCACAACAATACTCAGAA
Found at i:3671 original size:88 final size:88
Alignment explanation
Indices: 3522--3697 Score: 334
Period size: 88 Copynumber: 2.0 Consensus size: 88
3512 AAGCCTCGGG
3522 TCGGTTACAAAAACCATGCCCTATAAATGTTAACAAAATAACATTTGCTAAACAAATATCCTCAA
1 TCGGTTACAAAAACCATGCCCTATAAATGTTAACAAAATAACATTTGCTAAACAAATATCCTCAA
3587 GTTTTTGGCCCTGCCTTAGTGGT
66 GTTTTTGGCCCTGCCTTAGTGGT
*
3610 TCGGTTACAAAAACCATGCCCTGTAAATGTTAACAAAATAACATTTGCTAAACAAATATCCTCAA
1 TCGGTTACAAAAACCATGCCCTATAAATGTTAACAAAATAACATTTGCTAAACAAATATCCTCAA
*
3675 GTTTTTGGCCCTGGCTTAGTGGT
66 GTTTTTGGCCCTGCCTTAGTGGT
3698 AAGATTCCTT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (88 bp):
TCGGTTACAAAAACCATGCCCTATAAATGTTAACAAAATAACATTTGCTAAACAAATATCCTCAA
GTTTTTGGCCCTGCCTTAGTGGT
Found at i:5197 original size:40 final size:40
Alignment explanation
Indices: 5153--5559 Score: 608
Period size: 40 Copynumber: 10.2 Consensus size: 40
5143 TACGCGGCAC
* *
5153 ATTCACATTCAAATTTTCCAATTGACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
*
5193 ATTCACATCCAAATTTTCCAATTGACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
5233 CATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
1 -ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
* * *
5274 ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
* * *
5314 ATTCACATCCAACTTTCCCAAATAACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
*
5354 ATTCACATCCAAA-TTTCCAATAAACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
* *
5393 ATTCACATCCAAAATTTCCAAATAACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
*
5433 ATTCACATCCAAA-TTTCCAATAAACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
*
5472 ATTCACATCCAACA-TTTCCAAATAACATTGAACTTGCCTT
1 ATTCACATCCAA-ATTTTCCAATTAACATTGAACTTGCCTT
*
5512 ATTCACATCCAAA-TTTCCAA-TAGACATTGAACTTGCGTT
1 ATTCACATCCAAATTTTCCAATTA-ACATTGAACTTGCCTT
5551 AATTCACAT
1 -ATTCACAT
5560 TGGCCCTCAA
Statistics
Matches: 344, Mismatches: 18, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
38 2 0.01
39 95 0.28
40 208 0.60
41 39 0.11
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (40 bp):
ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
Found at i:5394 original size:79 final size:78
Alignment explanation
Indices: 5153--5559 Score: 634
Period size: 79 Copynumber: 5.1 Consensus size: 78
5143 TACGCGGCAC
* * * *
5153 ATTCACATTCAAATTTTCCAATTGACATTGAACTTGCCTTATTCACATCCAAATTTTCCAATTGA
1 ATTCACATCCAAA-TTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAA-TTTCCAATAGA
5218 CATTGAACTTGCCTT
64 CATTGAACTTGCCTT
* * *
5233 CATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTTATTCACATCCAACTTTCCCAATTG
1 -ATTCACATCCAAA-TTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTT-CCAATAG
5298 ACATTGAACTTGCCTT
63 ACATTGAACTTGCCTT
* *
5314 ATTCACATCCAACTTTCCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAAC
1 ATTCACATCCAAATTT-CCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAGAC
5379 ATTGAACTTGCCTT
65 ATTGAACTTGCCTT
*
5393 ATTCACATCCAAAATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAAC
1 ATTCACATCC-AAATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAGAC
5458 ATTGAACTTGCCTT
65 ATTGAACTTGCCTT
5472 ATTCACATCCAACATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAGAC
1 ATTCACATCCAA-ATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAGAC
*
5537 ATTGAACTTGCGTT
65 ATTGAACTTGCCTT
5551 AATTCACAT
1 -ATTCACAT
5560 TGGCCCTCAA
Statistics
Matches: 310, Mismatches: 11, Indels: 11
0.93 0.03 0.03
Matches are distributed among these distances:
78 2 0.01
79 170 0.55
80 65 0.21
81 73 0.24
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (78 bp):
ATTCACATCCAAATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAGACA
TTGAACTTGCCTT
Found at i:5430 original size:119 final size:117
Alignment explanation
Indices: 5153--5559 Score: 586
Period size: 119 Copynumber: 3.4 Consensus size: 117
5143 TACGCGGCAC
* * * * *
5153 ATTCACATTCAAATTTTCCAATTGACATTGAACTTGCCTTATTCACATCCAAATTTTCCAATTGA
1 ATTCACATCCAAA-TTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAA-TTTCCAAATAA
*
5218 CATTGAACTTGCCTTCATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
64 CATTGAACTTGCCTT-ATTCACATCCAAA-TTTCCAATAAACATTGAACTTGCCTT
* * * *
5274 ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTTATTCACATCCAACTTTCCCAAATAA
1 ATTCACATCCAAATTT-CCAAATAACATTGAACTTGCCTTATTCACATCCAAATTT-CCAAATAA
5339 CATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAACATTGAACTTGCCTT
64 CATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAACATTGAACTTGCCTT
5393 ATTCACATCCAAAATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCC-AATAAA
1 ATTCACATCC-AAATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAAAT-AA
5457 CATTGAACTTGCCTTATTCACATCCAACATTTCCAA-ATAACATTGAACTTGCCTT
64 CATTGAACTTGCCTTATTCACATCCAA-ATTTCCAATA-AACATTGAACTTGCCTT
*
5512 ATTCACATCCAAATTTCC-AATAGACATTGAACTTGCGTTAATTCACAT
1 ATTCACATCCAAATTTCCAAATA-ACATTGAACTTGCCTT-ATTCACAT
5560 TGGCCCTCAA
Statistics
Matches: 267, Mismatches: 11, Indels: 18
0.90 0.04 0.06
Matches are distributed among these distances:
117 7 0.03
118 55 0.21
119 114 0.43
120 24 0.09
121 67 0.25
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (117 bp):
ATTCACATCCAAATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAAATAACA
TTGAACTTGCCTTATTCACATCCAAATTTCCAATAAACATTGAACTTGCCTT
Done.